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ChristopherWilks / snaptron

fast webservices based query tool for large sets of genomic features
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GTEX hg19 availability #9

Closed marcDabad closed 3 years ago

marcDabad commented 5 years ago

Is there a possibility to change from GRCh38 to GRCh37(hg19) when we are querying GTEX?

lcolladotor commented 5 years ago

Hi @marcDabad,

I'm external to Snaptron, but I think that the answer is no.

That's because Snaptron is based on the Rail-RNA alignments that we used for creating recount2 https://www.nature.com/articles/nbt.3838 and those are hg38 based. Unless Chris lifted over exon-exon junctions from hg38 to hg19.

Best, Leonardo

ChristopherWilks commented 5 years ago

Hi @marcDabad,

Leonardo is correct.
All currently maintained Snaptron compilations (e.g. GTEx, TCGA, SRAv2) are on hg38. We currently don't have any plans to make hg19 versions available.

For my own research I usually liftover query junctions, if they came from hg19, before searching them against Snaptron. It's inconvenient but it usually works for the vast majority of them.

Chris